Police say the girl lay for eight hours among the bodies – apparently too scared to move.
The dead are believed to be a British family – a father, mother and grandmother.
Earlier a seven-year-old girl was discovered lying on the road in a critical condition near the BMW people carrier, while a male cyclist, who had also been shot, was found dead nearby.
Prosecutors said the girl of four was only found when investigators began a forensic examination of the car.
It was also reported that the girl was speaking English.
The BMW was discovered surrounded by spent bullet cartridges in a car park on the outskirts of a forest near Chevaline, at Lake Annecy, a region popular with tourists.
French officials said the British-registered vehicle was owned by a UK national who was staying at a campsite, believed to be in the Saint-Jorioz area.
Annecy prosecutor Eric Maillaud said: "The owner of the vehicle was the person who identified himself to the campsite.
"He is presumed to be a victim and was accompanied by two women and two little girls. We can assume it's a family although it is yet to be proved."
He added: "We have been taking evidence, including DNA, which will be sent to the British authorities for confirmation."
The prosecutor said 15 cartridges were found near the car. A "very large number" of shots had been fired.
The firearm used is thought to be an automatic pistol, he added.
Mr Maillaud said the scene was like something from in a film.
He added: "When the investigators got into the car they discovered a little (four-year-old) girl, who was frozen still and uninjured."
Mr Maillaud said the critically injured seven-year-old was taken to the Grenoble University Hospital where her condition had been stabilised following emergency surgery. Doctors say she is now out of danger, he added.
A FCO spokesman said British consular staff arrived in Grenoble this morning and were to liaise with French authorities.